......

workflow.wdl

@@ -10,31 +10,7 @@ import "./tasks/multiqc.wdl" as multiqc
 
 workflow {{ project_name }} {
 	
-	File inputSamplesFile
-	File idx
-	File screen_ref_dir
-	File fastq_screen_conf
-	File gtf
-	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
-	String fastp_docker
-	String adapter_sequence
-	String adapter_sequence_r2
-	String fastp_cluster
-	String umi_loc
-	String idx_prefix
-	String pen_intronlen
-	String fastqc_cluster_config
-	String fastqc_docker
-	String fastqscreen_docker
-	String fastqscreen_cluster_config
-	String hisat2_docker
-	String hisat2_cluster
-	String qualimapBAMqc_docker
-	String qualimapBAMqc_cluster_config
-	String qualimapRNAseq_docker
-	String qualimapRNAseq_cluster_config
-	String samtools_docker
-	String samtools_cluster
+	
 	String stringtie_docker
 	String stringtie_cluster
 	String multiqc_cluster_config
@@ -50,22 +26,5 @@ workflow {{ project_name }} {
 	Int length_required
 	Int umi_len
 	Int UMI
-	Int qualified_quality_phred
-	Int length_required1
-	Int disable_quality_filtering
-	Int pen_cansplice
-	Int pen_noncansplice
-	Int min_intronlen
-	Int max_intronlen
-	Int maxins
-	Int minins
-	Int fastqc_disk_size
-	Int fastqscreen_disk_size
-	Int qualimapBAMqc_disk_size
-	Int qualimapRNAseq_disk_size
-	Int insert_size
-	Int minimum_length_allowed_for_the_predicted_transcripts
-    	Int Junctions_no_spliced_reads
-   	Float minimum_isoform_abundance
-    	Float maximum_fraction_of_muliplelocationmapped_reads
+	
 }